LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
###############################################################################
# MD simulation for HDNNP water
###############################################################################

###############################################################################
# VARIABLES
###############################################################################
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Configuration files
variable cfgFile         string "data.H2O-360mol"
# Timesteps
variable numSteps        equal  10
variable dt              equal  0.0005
# HDNNP
variable hdnnpCutoff     equal  6.36
variable hdnnpDir        string "hdnnp-data"

###############################################################################
# GENERAL SETUP
###############################################################################
units metal
boundary p p p
atom_style atomic
read_data ${cfgFile}
read_data data.H2O-360mol
Reading data file ...
  orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  1080 atoms
  read_data CPU = 0.004 seconds
timestep ${dt}
timestep 0.0005
thermo 1

###############################################################################
# HDNNP
###############################################################################
pair_style hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_style hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
pair_coeff * * H O

###############################################################################
# INTEGRATOR
###############################################################################
fix INT all nve

###############################################################################
# OUTPUT
###############################################################################
# dump 1 all atom 1 dump.hdnnp

###############################################################################
# SIMULATION
###############################################################################
run ${numSteps}
run 10

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770

@Article{Singraber19,
 author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
 title = {Library-Based {LAMMPS} Implementation of High-Dimensional
    Neural Network Potentials},
 year = {2019},
 month = mar,
 volume = {15},
 pages = {1827--1840},
 doi = {10.1021/acs.jctc.8b00770},
 journal = {J.~Chem.\ Theory Comput.},
 number = {3}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE


*******************************************************************************

WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
------------------------------------------------------------------

n²p² version  (from git): patch_2Aug2023-264-g174825fe8c
             (version.h): v2.2.0
------------------------------------------------------------
Git branch              : collected-small-changes
Git revision            : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
Compile date/time       : Aug 23 2023 08:43:11
------------------------------------------------------------

Features/Flags:
------------------------------------------------------------
Symmetry function groups     : enabled
Symmetry function cache      : enabled
Timing function available    : available
Asymmetric polynomial SFs    : available
SF low neighbor number check : enabled
SF derivative memory layout  : reduced
MPI explicitly disabled      : no
------------------------------------------------------------

Please cite the following papers when publishing results obtained with n²p²:
-------------------------------------------------------------------------------
 * General citation for n²p² and the LAMMPS interface:

 Singraber, A.; Behler, J.; Dellago, C.
 Library-Based LAMMPS Implementation of High-Dimensional
 Neural Network Potentials.
 J. Chem. Theory Comput. 2019 15 (3), 1827–1840.
 https://doi.org/10.1021/acs.jctc.8b00770
-------------------------------------------------------------------------------
 * Additionally, if you use the NNP training features of n²p²:

 Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C.
 Parallel Multistream Training of High-Dimensional Neural
 Network Potentials.
 J. Chem. Theory Comput. 2019, 15 (5), 3075–3092.
 https://doi.org/10.1021/acs.jctc.8b01092
-------------------------------------------------------------------------------
 * Additionally, if polynomial symmetry functions are used:

 Bircher, M. P.; Singraber, A.; Dellago, C.
 Improved Description of Atomic Environments Using Low-Cost
 Polynomial Functions with Compact Support.
 arXiv:2010.14414 [cond-mat, physics:physics] 2020.
 https://arxiv.org/abs/2010.14414
*******************************************************************************

*** SETUP: SETTINGS FILE ******************************************************

Settings file name: hdnnp-data/input.nn
Read 120 lines.
Found 70 lines with keywords.
This settings file defines a short-range only NNP.
*******************************************************************************

*** SETUP: NORMALIZATION ******************************************************

Data set normalization is used.
Mean energy per atom     :  -2.5521343547039809E+01
Conversion factor energy :   2.4265748255366972E+02
Conversion factor length :   5.8038448995319847E+00
*******************************************************************************

*** SETUP: ELEMENT MAP ********************************************************

Number of element strings found: 2
Element  0:  H (  1)
Element  1:  O (  8)
*******************************************************************************

*** SETUP: ELEMENTS ***********************************************************

Number of elements is consistent: 2
Atomic energy offsets per element:
Element  0:   0.00000000E+00
Element  1:   0.00000000E+00
Energy offsets are automatically subtracted from reference energies.
*******************************************************************************

*** SETUP: CUTOFF FUNCTIONS ***************************************************

Parameter alpha for inner cutoff: 0.000000
Inner cutoff = Symmetry function cutoff * alpha
Equal cutoff function type for all symmetry functions:
CutoffFunction::CT_TANHU (2)
f(r) = tanh^3(1 - r/rc)
*******************************************************************************

*** SETUP: SYMMETRY FUNCTIONS *************************************************

Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.

Short range atomic symmetry functions element  H :
-------------------------------------------------------------------------------------------------
 ind ec tp sbtp e1 e2       eta      rs/rl         rc   angl   angr la zeta    a    ln
-------------------------------------------------------------------------------------------------
   1  H  2  ct2  H    1.000E-03  0.000E+00  1.200E+01                       0.00    51
   2  H  2  ct2  O    1.000E-03  0.000E+00  1.200E+01                       0.00    61
   3  H  2  ct2  H    1.000E-02  0.000E+00  1.200E+01                       0.00    52
   4  H  2  ct2  O    1.000E-02  0.000E+00  1.200E+01                       0.00    62
   5  H  2  ct2  H    3.000E-02  0.000E+00  1.200E+01                       0.00    53
   6  H  2  ct2  O    3.000E-02  0.000E+00  1.200E+01                       0.00    63
   7  H  2  ct2  H    6.000E-02  0.000E+00  1.200E+01                       0.00    54
   8  H  2  ct2  O    6.000E-02  0.000E+00  1.200E+01                       0.00    64
   9  H  2  ct2  O    1.500E-01  9.000E-01  1.200E+01                       0.00    65
  10  H  2  ct2  H    1.500E-01  1.900E+00  1.200E+01                       0.00    55
  11  H  2  ct2  O    3.000E-01  9.000E-01  1.200E+01                       0.00    66
  12  H  2  ct2  H    3.000E-01  1.900E+00  1.200E+01                       0.00    56
  13  H  2  ct2  O    6.000E-01  9.000E-01  1.200E+01                       0.00    67
  14  H  2  ct2  H    6.000E-01  1.900E+00  1.200E+01                       0.00    57
  15  H  2  ct2  O    1.500E+00  9.000E-01  1.200E+01                       0.00    68
  16  H  2  ct2  H    1.500E+00  1.900E+00  1.200E+01                       0.00    58
  17  H  3  ct2  O  O 1.000E-03  0.000E+00  1.200E+01               -1  4.0 0.00   115
  18  H  3  ct2  O  O 1.000E-03  0.000E+00  1.200E+01                1  4.0 0.00   114
  19  H  3  ct2  H  O 1.000E-02  0.000E+00  1.200E+01               -1  4.0 0.00   105
  20  H  3  ct2  H  O 1.000E-02  0.000E+00  1.200E+01                1  4.0 0.00   103
  21  H  3  ct2  H  O 3.000E-02  0.000E+00  1.200E+01               -1  1.0 0.00   100
  22  H  3  ct2  O  O 3.000E-02  0.000E+00  1.200E+01               -1  1.0 0.00   113
  23  H  3  ct2  H  O 3.000E-02  0.000E+00  1.200E+01                1  1.0 0.00    98
  24  H  3  ct2  O  O 3.000E-02  0.000E+00  1.200E+01                1  1.0 0.00   112
  25  H  3  ct2  H  O 7.000E-02  0.000E+00  1.200E+01               -1  1.0 0.00    95
  26  H  3  ct2  H  O 7.000E-02  0.000E+00  1.200E+01                1  1.0 0.00    93
  27  H  3  ct2  H  O 2.000E-01  0.000E+00  1.200E+01                1  1.0 0.00    90
-------------------------------------------------------------------------------------------------
Short range atomic symmetry functions element  O :
-------------------------------------------------------------------------------------------------
 ind ec tp sbtp e1 e2       eta      rs/rl         rc   angl   angr la zeta    a    ln
-------------------------------------------------------------------------------------------------
   1  O  2  ct2  H    1.000E-03  0.000E+00  1.200E+01                       0.00    70
   2  O  2  ct2  O    1.000E-03  0.000E+00  1.200E+01                       0.00    80
   3  O  2  ct2  H    1.000E-02  0.000E+00  1.200E+01                       0.00    71
   4  O  2  ct2  O    1.000E-02  0.000E+00  1.200E+01                       0.00    81
   5  O  2  ct2  H    3.000E-02  0.000E+00  1.200E+01                       0.00    72
   6  O  2  ct2  O    3.000E-02  0.000E+00  1.200E+01                       0.00    82
   7  O  2  ct2  H    6.000E-02  0.000E+00  1.200E+01                       0.00    73
   8  O  2  ct2  O    6.000E-02  0.000E+00  1.200E+01                       0.00    83
   9  O  2  ct2  H    1.500E-01  9.000E-01  1.200E+01                       0.00    74
  10  O  2  ct2  O    1.500E-01  4.000E+00  1.200E+01                       0.00    84
  11  O  2  ct2  H    3.000E-01  9.000E-01  1.200E+01                       0.00    75
  12  O  2  ct2  O    3.000E-01  4.000E+00  1.200E+01                       0.00    85
  13  O  2  ct2  H    6.000E-01  9.000E-01  1.200E+01                       0.00    76
  14  O  2  ct2  O    6.000E-01  4.000E+00  1.200E+01                       0.00    86
  15  O  2  ct2  H    1.500E+00  9.000E-01  1.200E+01                       0.00    77
  16  O  2  ct2  O    1.500E+00  4.000E+00  1.200E+01                       0.00    87
  17  O  3  ct2  H  O 1.000E-03  0.000E+00  1.200E+01               -1  4.0 0.00   110
  18  O  3  ct2  O  O 1.000E-03  0.000E+00  1.200E+01               -1  4.0 0.00   120
  19  O  3  ct2  H  O 1.000E-03  0.000E+00  1.200E+01                1  4.0 0.00   109
  20  O  3  ct2  O  O 1.000E-03  0.000E+00  1.200E+01                1  4.0 0.00   119
  21  O  3  ct2  H  H 1.000E-02  0.000E+00  1.200E+01               -1  4.0 0.00   104
  22  O  3  ct2  H  H 1.000E-02  0.000E+00  1.200E+01                1  4.0 0.00   102
  23  O  3  ct2  H  H 3.000E-02  0.000E+00  1.200E+01               -1  1.0 0.00    99
  24  O  3  ct2  H  O 3.000E-02  0.000E+00  1.200E+01               -1  1.0 0.00   108
  25  O  3  ct2  O  O 3.000E-02  0.000E+00  1.200E+01               -1  1.0 0.00   118
  26  O  3  ct2  H  H 3.000E-02  0.000E+00  1.200E+01                1  1.0 0.00    97
  27  O  3  ct2  H  O 3.000E-02  0.000E+00  1.200E+01                1  1.0 0.00   107
  28  O  3  ct2  O  O 3.000E-02  0.000E+00  1.200E+01                1  1.0 0.00   117
  29  O  3  ct2  H  H 7.000E-02  0.000E+00  1.200E+01               -1  1.0 0.00    94
  30  O  3  ct2  H  H 7.000E-02  0.000E+00  1.200E+01                1  1.0 0.00    92
-------------------------------------------------------------------------------------------------
Minimum cutoff radius for element  H: 12.000000
Minimum cutoff radius for element  O: 12.000000
Maximum cutoff radius (global)      : 12.000000
*******************************************************************************

*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************

Symmetry function derivatives memory table for element  H :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
-  H:   15 of   27 ( 55.6 %)
-  O:   19 of   27 ( 70.4 %)
-------------------------------------------------------------------------------
Symmetry function derivatives memory table for element  O :
-------------------------------------------------------------------------------
Relevant symmetry functions for neighbors with element:
-  H:   18 of   30 ( 60.0 %)
-  O:   16 of   30 ( 53.3 %)
-------------------------------------------------------------------------------
*******************************************************************************

*** SETUP: SYMMETRY FUNCTION CACHE ********************************************

Element  H: in total 4 caches, used 17.00 times on average.
Element  O: in total 4 caches, used 17.00 times on average.
*******************************************************************************

*** SETUP: SYMMETRY FUNCTION GROUPS *******************************************

Abbreviations:
--------------
ind .... Symmetry function index.
ec ..... Central atom element.
tp ..... Symmetry function type.
sbtp ... Symmetry function subtype (e.g. cutoff type).
e1 ..... Neighbor 1 element.
e2 ..... Neighbor 2 element.
eta .... Gaussian width eta.
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
angl.... Left cutoff angle for polynomial.
angr.... Right cutoff angle for polynomial.
la ..... Angle prefactor lambda.
zeta ... Angle term exponent zeta.
rc ..... Cutoff radius / right cutoff radius for polynomial.
a ...... Free parameter alpha (e.g. cutoff alpha).
ln ..... Line number in settings file.
mi ..... Member index.
sfi .... Symmetry function index.
e ...... Recalculate exponential term.

Short range atomic symmetry function groups element  H :
----------------------------------------------------------------------------------------------------------
 ind ec tp sbtp e1 e2       eta      rs/rl         rc   angl   angr la zeta    a    ln   mi  sfi e
----------------------------------------------------------------------------------------------------------
   1  H  2  ct2  H            *          *  1.200E+01                       0.00     *    *    *  
   -  -  -    -  -    1.000E-03  0.000E+00          -                          -    51    1    1  
   -  -  -    -  -    1.000E-02  0.000E+00          -                          -    52    2    3  
   -  -  -    -  -    3.000E-02  0.000E+00          -                          -    53    3    5  
   -  -  -    -  -    6.000E-02  0.000E+00          -                          -    54    4    7  
   -  -  -    -  -    1.500E-01  1.900E+00          -                          -    55    5   10  
   -  -  -    -  -    3.000E-01  1.900E+00          -                          -    56    6   12  
   -  -  -    -  -    6.000E-01  1.900E+00          -                          -    57    7   14  
   -  -  -    -  -    1.500E+00  1.900E+00          -                          -    58    8   16  
   2  H  2  ct2  O            *          *  1.200E+01                       0.00     *    *    *  
   -  -  -    -  -    1.000E-03  0.000E+00          -                          -    61    1    2  
   -  -  -    -  -    1.000E-02  0.000E+00          -                          -    62    2    4  
   -  -  -    -  -    3.000E-02  0.000E+00          -                          -    63    3    6  
   -  -  -    -  -    6.000E-02  0.000E+00          -                          -    64    4    8  
   -  -  -    -  -    1.500E-01  9.000E-01          -                          -    65    5    9  
   -  -  -    -  -    3.000E-01  9.000E-01          -                          -    66    6   11  
   -  -  -    -  -    6.000E-01  9.000E-01          -                          -    67    7   13  
   -  -  -    -  -    1.500E+00  9.000E-01          -                          -    68    8   15  
   3  H  3  ct2  H  O         *          *  1.200E+01                *    * 0.00     *    *    * *
   -  -  -    -  -  - 1.000E-02  0.000E+00          -               -1  4.0    -   105    1   19 1
   -  -  -    -  -  - 1.000E-02  0.000E+00          -                1  4.0    -   103    2   20 0
   -  -  -    -  -  - 3.000E-02  0.000E+00          -               -1  1.0    -   100    3   21 1
   -  -  -    -  -  - 3.000E-02  0.000E+00          -                1  1.0    -    98    4   23 0
   -  -  -    -  -  - 7.000E-02  0.000E+00          -               -1  1.0    -    95    5   25 1
   -  -  -    -  -  - 7.000E-02  0.000E+00          -                1  1.0    -    93    6   26 0
   -  -  -    -  -  - 2.000E-01  0.000E+00          -                1  1.0    -    90    7   27 1
   4  H  3  ct2  O  O         *          *  1.200E+01                *    * 0.00     *    *    * *
   -  -  -    -  -  - 1.000E-03  0.000E+00          -               -1  4.0    -   115    1   17 1
   -  -  -    -  -  - 1.000E-03  0.000E+00          -                1  4.0    -   114    2   18 0
   -  -  -    -  -  - 3.000E-02  0.000E+00          -               -1  1.0    -   113    3   22 1
   -  -  -    -  -  - 3.000E-02  0.000E+00          -                1  1.0    -   112    4   24 0
----------------------------------------------------------------------------------------------------------
Short range atomic symmetry function groups element  O :
----------------------------------------------------------------------------------------------------------
 ind ec tp sbtp e1 e2       eta      rs/rl         rc   angl   angr la zeta    a    ln   mi  sfi e
----------------------------------------------------------------------------------------------------------
   1  O  2  ct2  H            *          *  1.200E+01                       0.00     *    *    *  
   -  -  -    -  -    1.000E-03  0.000E+00          -                          -    70    1    1  
   -  -  -    -  -    1.000E-02  0.000E+00          -                          -    71    2    3  
   -  -  -    -  -    3.000E-02  0.000E+00          -                          -    72    3    5  
   -  -  -    -  -    6.000E-02  0.000E+00          -                          -    73    4    7  
   -  -  -    -  -    1.500E-01  9.000E-01          -                          -    74    5    9  
   -  -  -    -  -    3.000E-01  9.000E-01          -                          -    75    6   11  
   -  -  -    -  -    6.000E-01  9.000E-01          -                          -    76    7   13  
   -  -  -    -  -    1.500E+00  9.000E-01          -                          -    77    8   15  
   2  O  2  ct2  O            *          *  1.200E+01                       0.00     *    *    *  
   -  -  -    -  -    1.000E-03  0.000E+00          -                          -    80    1    2  
   -  -  -    -  -    1.000E-02  0.000E+00          -                          -    81    2    4  
   -  -  -    -  -    3.000E-02  0.000E+00          -                          -    82    3    6  
   -  -  -    -  -    6.000E-02  0.000E+00          -                          -    83    4    8  
   -  -  -    -  -    1.500E-01  4.000E+00          -                          -    84    5   10  
   -  -  -    -  -    3.000E-01  4.000E+00          -                          -    85    6   12  
   -  -  -    -  -    6.000E-01  4.000E+00          -                          -    86    7   14  
   -  -  -    -  -    1.500E+00  4.000E+00          -                          -    87    8   16  
   3  O  3  ct2  H  H         *          *  1.200E+01                *    * 0.00     *    *    * *
   -  -  -    -  -  - 1.000E-02  0.000E+00          -               -1  4.0    -   104    1   21 1
   -  -  -    -  -  - 1.000E-02  0.000E+00          -                1  4.0    -   102    2   22 0
   -  -  -    -  -  - 3.000E-02  0.000E+00          -               -1  1.0    -    99    3   23 1
   -  -  -    -  -  - 3.000E-02  0.000E+00          -                1  1.0    -    97    4   26 0
   -  -  -    -  -  - 7.000E-02  0.000E+00          -               -1  1.0    -    94    5   29 1
   -  -  -    -  -  - 7.000E-02  0.000E+00          -                1  1.0    -    92    6   30 0
   4  O  3  ct2  H  O         *          *  1.200E+01                *    * 0.00     *    *    * *
   -  -  -    -  -  - 1.000E-03  0.000E+00          -               -1  4.0    -   110    1   17 1
   -  -  -    -  -  - 1.000E-03  0.000E+00          -                1  4.0    -   109    2   19 0
   -  -  -    -  -  - 3.000E-02  0.000E+00          -               -1  1.0    -   108    3   24 1
   -  -  -    -  -  - 3.000E-02  0.000E+00          -                1  1.0    -   107    4   27 0
   5  O  3  ct2  O  O         *          *  1.200E+01                *    * 0.00     *    *    * *
   -  -  -    -  -  - 1.000E-03  0.000E+00          -               -1  4.0    -   120    1   18 1
   -  -  -    -  -  - 1.000E-03  0.000E+00          -                1  4.0    -   119    2   20 0
   -  -  -    -  -  - 3.000E-02  0.000E+00          -               -1  1.0    -   118    3   25 1
   -  -  -    -  -  - 3.000E-02  0.000E+00          -                1  1.0    -   117    4   28 0
----------------------------------------------------------------------------------------------------------
*******************************************************************************

*** SETUP: NEURAL NETWORKS ****************************************************

Normalize neurons (all elements): 0
-------------------------------------------------------------------------------
Atomic short range NN for element  H :
Number of weights    :   1325
Number of biases     :     51
Number of connections:   1376
Architecture       27   25   25    1
-------------------------------------------------------------------------------
   1   G   t   t   l
   2   G   t   t    
   3   G   t   t    
   4   G   t   t    
   5   G   t   t    
   6   G   t   t    
   7   G   t   t    
   8   G   t   t    
   9   G   t   t    
  10   G   t   t    
  11   G   t   t    
  12   G   t   t    
  13   G   t   t    
  14   G   t   t    
  15   G   t   t    
  16   G   t   t    
  17   G   t   t    
  18   G   t   t    
  19   G   t   t    
  20   G   t   t    
  21   G   t   t    
  22   G   t   t    
  23   G   t   t    
  24   G   t   t    
  25   G   t   t    
  26   G            
  27   G            
-------------------------------------------------------------------------------
Atomic short range NN for element  O :
Number of weights    :   1400
Number of biases     :     51
Number of connections:   1451
Architecture       30   25   25    1
-------------------------------------------------------------------------------
   1   G   t   t   l
   2   G   t   t    
   3   G   t   t    
   4   G   t   t    
   5   G   t   t    
   6   G   t   t    
   7   G   t   t    
   8   G   t   t    
   9   G   t   t    
  10   G   t   t    
  11   G   t   t    
  12   G   t   t    
  13   G   t   t    
  14   G   t   t    
  15   G   t   t    
  16   G   t   t    
  17   G   t   t    
  18   G   t   t    
  19   G   t   t    
  20   G   t   t    
  21   G   t   t    
  22   G   t   t    
  23   G   t   t    
  24   G   t   t    
  25   G   t   t    
  26   G            
  27   G            
  28   G            
  29   G            
  30   G            
-------------------------------------------------------------------------------
*******************************************************************************

*** SETUP: SYMMETRY FUNCTION SCALING ******************************************

Equal scaling type for all symmetry functions:
Scaling type::ST_SCALECENTER (3)
Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin)
Smin = 0.000000
Smax = 1.000000
Symmetry function scaling statistics from file: hdnnp-data/scaling.data
-------------------------------------------------------------------------------

Abbreviations:
--------------
ind ..... Symmetry function index.
min ..... Minimum symmetry function value.
max ..... Maximum symmetry function value.
mean .... Mean symmetry function value.
sigma ... Standard deviation of symmetry function values.
sf ...... Scaling factor for derivatives.
Smin .... Desired minimum scaled symmetry function value.
Smax .... Desired maximum scaled symmetry function value.
t ....... Scaling type.

Scaling data for symmetry functions element  H :
-------------------------------------------------------------------------------
 ind       min       max      mean     sigma        sf  Smin  Smax t
-------------------------------------------------------------------------------
   1  1.09E+00  9.62E+00  2.27E+00  6.79E-01  1.17E-01  0.00  1.00 3
   2  7.33E-01  5.00E+00  1.33E+00  3.39E-01  2.34E-01  0.00  1.00 3
   3  7.60E-01  7.14E+00  1.65E+00  5.08E-01  1.57E-01  0.00  1.00 3
   4  5.48E-01  3.77E+00  1.02E+00  2.54E-01  3.11E-01  0.00  1.00 3
   5  4.01E-01  4.15E+00  9.09E-01  2.98E-01  2.67E-01  0.00  1.00 3
   6  3.62E-01  2.27E+00  6.49E-01  1.48E-01  5.25E-01  0.00  1.00 3
   7  1.89E-01  2.23E+00  4.57E-01  1.60E-01  4.90E-01  0.00  1.00 3
   8  2.67E-01  1.32E+00  4.24E-01  8.05E-02  9.49E-01  0.00  1.00 3
   9  2.45E-01  9.48E-01  3.62E-01  5.30E-02  1.42E+00  0.00  1.00 3
  10  2.22E-01  2.76E+00  5.39E-01  2.01E-01  3.94E-01  0.00  1.00 3
  11  1.47E-01  5.56E-01  2.68E-01  2.62E-02  2.45E+00  0.00  1.00 3
  12  9.91E-02  1.73E+00  2.96E-01  1.16E-01  6.14E-01  0.00  1.00 3
  13  6.51E-02  3.45E-01  1.85E-01  1.97E-02  3.57E+00  0.00  1.00 3
  14  3.17E-02  9.13E-01  1.50E-01  5.35E-02  1.13E+00  0.00  1.00 3
  15  2.92E-03  2.65E-01  7.65E-02  1.88E-02  3.82E+00  0.00  1.00 3
  16  3.21E-04  2.87E-01  4.58E-02  2.33E-02  3.49E+00  0.00  1.00 3
  17  2.47E-04  1.38E-01  1.77E-02  9.75E-03  7.23E+00  0.00  1.00 3
  18  5.10E-03  5.83E-01  2.39E-02  3.78E-02  1.73E+00  0.00  1.00 3
  19  3.23E-04  2.16E-01  1.71E-02  1.40E-02  4.63E+00  0.00  1.00 3
  20  4.96E-02  1.69E+00  1.45E-01  1.10E-01  6.11E-01  0.00  1.00 3
  21  3.41E-03  3.16E-01  1.84E-02  2.01E-02  3.20E+00  0.00  1.00 3
  22  1.31E-04  1.03E-01  6.37E-03  6.61E-03  9.76E+00  0.00  1.00 3
  23  3.38E-02  9.16E-01  8.13E-02  5.79E-02  1.13E+00  0.00  1.00 3
  24  4.17E-04  1.58E-01  4.66E-03  9.86E-03  6.35E+00  0.00  1.00 3
  25  7.35E-04  5.92E-02  3.70E-03  3.31E-03  1.71E+01  0.00  1.00 3
  26  8.98E-03  1.94E-01  2.41E-02  1.10E-02  5.40E+00  0.00  1.00 3
  27  2.12E-04  8.78E-03  2.06E-03  5.88E-04  1.17E+02  0.00  1.00 3
-------------------------------------------------------------------------------
Scaling data for symmetry functions element  O :
-------------------------------------------------------------------------------
 ind       min       max      mean     sigma        sf  Smin  Smax t
-------------------------------------------------------------------------------
   1  1.51E+00  1.00E+01  2.65E+00  6.78E-01  1.18E-01  0.00  1.00 3
   2  4.44E-01  4.62E+00  9.66E-01  3.37E-01  2.39E-01  0.00  1.00 3
   3  1.19E+00  7.53E+00  2.03E+00  5.06E-01  1.58E-01  0.00  1.00 3
   4  2.76E-01  3.39E+00  6.59E-01  2.50E-01  3.21E-01  0.00  1.00 3
   5  8.06E-01  4.54E+00  1.30E+00  2.94E-01  2.68E-01  0.00  1.00 3
   6  1.05E-01  1.89E+00  3.07E-01  1.42E-01  5.60E-01  0.00  1.00 3
   7  5.69E-01  2.62E+00  8.48E-01  1.57E-01  4.89E-01  0.00  1.00 3
   8  2.33E-02  9.36E-01  1.11E-01  6.98E-02  1.10E+00  0.00  1.00 3
   9  5.14E-01  1.85E+00  7.25E-01  9.80E-02  7.46E-01  0.00  1.00 3
  10  1.11E-01  2.91E+00  4.75E-01  2.34E-01  3.57E-01  0.00  1.00 3
  11  3.53E-01  1.07E+00  5.35E-01  4.52E-02  1.39E+00  0.00  1.00 3
  12  3.04E-02  2.53E+00  3.17E-01  2.10E-01  4.00E-01  0.00  1.00 3
  13  1.60E-01  6.63E-01  3.70E-01  3.08E-02  1.99E+00  0.00  1.00 3
  14  2.78E-03  2.30E+00  1.77E-01  1.86E-01  4.35E-01  0.00  1.00 3
  15  9.56E-03  3.91E-01  1.53E-01  2.79E-02  2.62E+00  0.00  1.00 3
  16  3.75E-06  2.04E+00  5.41E-02  1.43E-01  4.91E-01  0.00  1.00 3
  17  2.47E-03  3.43E-01  1.67E-02  2.19E-02  2.93E+00  0.00  1.00 3
  18  1.74E-05  5.63E-02  9.55E-04  3.36E-03  1.78E+01  0.00  1.00 3
  19  5.48E-02  3.02E+00  2.04E-01  2.01E-01  3.37E-01  0.00  1.00 3
  20  1.38E-03  4.99E-01  1.28E-02  3.18E-02  2.01E+00  0.00  1.00 3
  21  6.69E-03  2.67E-01  3.09E-02  1.71E-02  3.84E+00  0.00  1.00 3
  22  1.70E-02  1.42E+00  7.63E-02  9.29E-02  7.14E-01  0.00  1.00 3
  23  1.98E-02  4.08E-01  4.88E-02  2.55E-02  2.58E+00  0.00  1.00 3
  24  5.28E-04  2.33E-01  7.21E-03  1.45E-02  4.30E+00  0.00  1.00 3
  25  1.11E-05  3.53E-02  4.25E-04  2.05E-03  2.83E+01  0.00  1.00 3
  26  1.60E-02  8.22E-01  5.08E-02  5.28E-02  1.24E+00  0.00  1.00 3
  27  3.99E-03  7.86E-01  3.69E-02  5.05E-02  1.28E+00  0.00  1.00 3
  28  4.05E-05  9.84E-02  1.21E-03  5.79E-03  1.02E+01  0.00  1.00 3
  29  6.04E-03  9.93E-02  1.62E-02  5.52E-03  1.07E+01  0.00  1.00 3
  30  2.96E-03  1.55E-01  1.16E-02  8.94E-03  6.59E+00  0.00  1.00 3
-------------------------------------------------------------------------------
*******************************************************************************

*** SETUP: SYMMETRY FUNCTION STATISTICS ***************************************

Equal symmetry function statistics for all elements.
Collect min/max/mean/sigma                        : 0
Collect extrapolation warnings                    : 1
Write extrapolation warnings immediately to stderr: 0
Halt on any extrapolation warning                 : 0
*******************************************************************************

*** SETUP: NEURAL NETWORK WEIGHTS *********************************************

Short  NN weight file name format: hdnnp-data/weights.%03d.data
Setting short  NN weights for element  H from file: hdnnp-data/weights.001.data
Setting short  NN weights for element  O from file: hdnnp-data/weights.008.data
*******************************************************************************

*** SETUP: LAMMPS INTERFACE ***************************************************

Individual extrapolation warnings will not be shown.
Extrapolation warning summary will be shown every 5 timesteps.
The simulation will be stopped when 100 extrapolation warnings are exceeded.
Extrapolation warnings are accumulated over all time steps.
-------------------------------------------------------------------------------
CAUTION: If the LAMMPS unit system differs from the one used
         during NN training, appropriate conversion factors
         must be provided (see keywords cflength and cfenergy).

Length unit conversion factor:   1.8897261327999999E+00
Energy unit conversion factor:   3.6749325399999998E-02

Checking consistency of cutoff radii (in LAMMPS units):
LAMMPS Cutoff (via pair_coeff)  :   6.360E+00
Maximum symmetry function cutoff:   6.350E+00
Cutoff radii are consistent.
-------------------------------------------------------------------------------
Element mapping string from LAMMPS to n2p2: "1:H,2:O"

CAUTION: Please ensure that this mapping between LAMMPS
         atom types and NNP elements is consistent:

---------------------------
LAMMPS type  |  NNP element
---------------------------
          1 <->  H (  1)
          2 <->  O (  8)
---------------------------

NNP setup for LAMMPS completed.
*******************************************************************************
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.36
  ghost atom cutoff = 8.36
  binsize = 4.18, bins = 6 6 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair hdnnp, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
### NNP EW SUMMARY ### TS:          0 EW          0 EWPERSTEP  0.000e+00
Per MPI rank memory allocation (min/avg/max) = 4.021 | 4.021 | 4.021 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -750069.48      0             -750069.48     -5297.5537    
         1   8.5815594     -750070.71      0             -750069.51     -5249.2914    
         2   30.988787     -750073.91      0             -750069.59     -5023.6945    
         3   58.859866     -750077.88      0             -750069.67     -4427.8346    
         4   82.576399     -750081.26      0             -750069.74     -3275.4378    
### NNP EW SUMMARY ### TS:          5 EW          0 EWPERSTEP  0.000e+00
         5   94.968097     -750083.01      0             -750069.76     -1511.6733    
         6   93.724286     -750082.8       0             -750069.73      709.20465    
         7   82.243957     -750081.13      0             -750069.66      3020.5084    
         8   68.611429     -750079.14      0             -750069.57      4922.5176    
         9   62.314385     -750078.21      0             -750069.51      5933.1543    
### NNP EW SUMMARY ### TS:         10 EW          0 EWPERSTEP  0.000e+00
        10   69.501045     -750079.21      0             -750069.52      5761.8646    
Loop time of 3.2801 on 1 procs for 10 steps with 1080 atoms

Performance: 0.132 ns/day, 182.228 hours/ns, 3.049 timesteps/s, 3.293 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.2794     | 3.2794     | 3.2794     |   0.0 | 99.98
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00030785 | 0.00030785 | 0.00030785 |   0.0 |  0.01
Output  | 0.00018531 | 0.00018531 | 0.00018531 |   0.0 |  0.01
Modify  | 0.00013118 | 0.00013118 | 0.00013118 |   0.0 |  0.00
Other   |            | 9.142e-05  |            |       |  0.00

Nlocal:           1080 ave        1080 max        1080 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           4536 ave        4536 max        4536 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:       239270 ave      239270 max      239270 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 239270
Ave neighs/atom = 221.5463
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03
